Difference between revisions of "ABySS"
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|{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}} | |{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}} | ||
<!--Choose sections to enable - OPTIONAL--> | <!--Choose sections to enable - OPTIONAL--> | ||
| − | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> |
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
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ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. | ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
===Serial=== | ===Serial=== | ||
* {{#var:app}} | * {{#var:app}} | ||
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* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default: | |
| + | |||
| + | export HPC_USE_MPIEXEC=1 | ||
| + | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Revision as of 14:35, 6 September 2018
Description
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
Environment Modules
Run module spider abyss to find out what environment modules are available for this application.
Serial
- abyss
Parallel (MPI)
- intel/2016.0.109
- openmpi/1.10.2
- abyss/1.9.0
System Variables
- HPC_{{#uppercase:abyss}}_DIR - installation directory
How To Run
The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default:
export HPC_USE_MPIEXEC=1